Int. J. Mol. Sci. 2010, 11(10), 3725-3747; doi:10.3390/ijms11103725
Article

Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction

1,2,3email, 1,2email and 1,2,3,4,* email
1 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA 2 Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA 3 Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA 4 Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
* Author to whom correspondence should be addressed.
Received: 3 September 2010; in revised form: 10 September 2010 / Accepted: 15 September 2010 / Published: 29 September 2010
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Abstract: Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying MoRF-based protein-protein interactions. The method of reverse sequence alignment is also rationalized here as a novel approach for finding additional interaction regions, leading to the concept of a retro-MoRF, which has the reversed sequence of an identified MoRF. The set of retro-MoRF binding partners likely overlap the partner-sets of the originally identified MoRFs. The high abundance of MoRF-containing intrinsically disordered proteins in nature suggests the possibility that the number of retro-MoRFs could likewise be very high. This hypothesis provides new grounds for exploring the mysteries of protein-protein interaction networks at the genome level.
Keywords: reverse; retro; invert; alignment; intrinsic disorder; PONDR-RIBS

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MDPI and ACS Style

Xue, B.; Dunker, A.K.; Uversky, V.N. Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction. Int. J. Mol. Sci. 2010, 11, 3725-3747.

AMA Style

Xue B, Dunker AK, Uversky VN. Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction. International Journal of Molecular Sciences. 2010; 11(10):3725-3747.

Chicago/Turabian Style

Xue, Bin; Dunker, A. Keith; Uversky, Vladimir N. 2010. "Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction." Int. J. Mol. Sci. 11, no. 10: 3725-3747.

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